David Jones

This study uses pan-cancer phosphoproteomics to identify therapeutic targets and improve precision oncology by analyzing 1,998 tumor samples and developing new scores for kinase activity and immune response.

This study identifies local translation as a driver of glioblastoma tumor microtubes and invasion by linking subcellular protein synthesis to invasive cell states.

This paper creates a multi-omics atlas of human hindbrain development, revealing cellular diversity, regulatory programs, and disease relevance.

The paper introduces a PDX platform for pediatric cancers, providing in vivo drug testing models and molecular data to aid in therapy development.

The paper identifies SMARCAL1 as a novel predisposition gene for osteosarcoma by analyzing germline variants in DNA damage repair genes across childhood cancer cases.

This study identifies FGFR alterations in pediatric gliomas, their association with specific histologies, and their response to targeted therapies.

The paper uses single-cell technologies to show that large-scale chromosomal aberrations drive medulloblastoma initiation, while single-gene oncogenic events like MYC contribute to progression and therapy resistance.

This study identifies cell-state plasticity as a driver of heterogeneity in Group 3/4 medulloblastomas, showing that transcription factor perturbation can redirect tumor cells along different differentiation trajectories.

The paper identifies four immune clusters in pediatric nervous system tumors using RNA-seq data and validates them with multiple methods, highlighting the need for personalized immunogenomic profiling.

This study integrates phospho-proteogenomic and single-cell transcriptomic data to subtype meningiomas and identify subtype-specific immune infiltration patterns.

The paper identifies ROS1 fusions in various glioma types through genomic and transcriptomic analysis, showing they are not restricted to specific subtypes.

This study identifies genomic and methylation patterns associated with benign metastases and malignant transformation in giant cell tumour of bone.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

confFuse identifies high-confidence fusion genes from RNA-seq data by scoring candidates based on structural motifs, reducing false positives while maintaining high accuracy.

This study identifies ALT markers and mechanisms in pediatric glioblastoma using genomic and telomere features, revealing non-canonical ALT and a reliable classification scheme.

This study compares whole genome sequencing pipelines across five centers using a uniform tumor-normal sample pair, identifying factors affecting output consistency.